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I personally believe it's dependant on the use. If they are short sound fx, I use WAV settings and let flash compress accordingly. Background loops and music samples benefit greatly from MP3 compression (16kbps for tolerable and 32/64kbps for higer quality)

Wait a second. I was always under the impression that whatever the quality and type of your import audio, Flash would compress according to the publish settings. In other words, it wouldn't matter whether you imported compressed mp3s or wavs in to Flash editor. They would always publish according to Flash settings. Therefore I fail to see the benefit at import of selecting a different format.

I can however see the benefit of compressing short SFX wavs/mp3s less on export to retain quality by using different settings for your event sounds compression and streamed sounds compression. Is this what you meant?